Transmission-acceleration dengue outbreak-detection pipeline: a step-by-step computational protocol v2

<p>This protocol describes the end-to-end computational pipeline used to evaluate transmission-acceleration detectors against the rolling-baseline endemic-channel outbreak threshold for seasonal dengue. The pipeline is implemented as six sequential R scripts, organized under a shared configuration and detector library, that derive the constant transmission-acceleration activation and deactivation thresholds on the Quezon City series, run an independent robustness check on the detector's window widths, characterise outbreak-threshold drift, run the city-scale analysis, and apply the framework without parameter modification to seventeen Philippine administrative regions and to eight dengue-endemic countries. It evaluates fourteen detectors across four paradigms against an anticipatory anchor framework, computes eight performance metrics, and runs a year-cluster bootstrap consensus analysis. Following the steps reproduces every figure, table, and CSV output of the companion manuscript from the deposited dataset. The pipeline consumes only the weekly dengue case series and requires no climate covariates, line-list data, or model-fitting infrastructure beyond a single workstation running R.</p>